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- PDB-6eoa: Crystal Structure of HAL3 from Cryptococcus neoformans -

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Basic information

Entry
Database: PDB / ID: 6eoa
TitleCrystal Structure of HAL3 from Cryptococcus neoformans
ComponentsPhosphopantothenoylcysteine decarboxylase
KeywordsFLAVOPROTEIN / FMN / phosphopantothenoylcysteine decarboxylase (PPCDC) enzyme
Function / homology
Function and homology information


coenzyme A biosynthetic process / catalytic activity / nucleotide binding
Similarity search - Function
Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Phosphopantothenoylcysteine decarboxylase
Similarity search - Component
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsReverter, D. / Zhang, C. / Molero, C. / Arino, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-66417-P Spain
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Characterization of the atypical Ppz/Hal3 phosphatase system from the pathogenic fungus Cryptococcus neoformans.
Authors: Zhang, C. / Garcia-Rodas, R. / Molero, C. / de Oliveira, H.C. / Tabernero, L. / Reverter, D. / Zaragoza, O. / Arino, J.
History
DepositionOct 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphopantothenoylcysteine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5572
Polymers35,1001
Non-polymers4561
Water36020
1
A: Phosphopantothenoylcysteine decarboxylase
hetero molecules

A: Phosphopantothenoylcysteine decarboxylase
hetero molecules

A: Phosphopantothenoylcysteine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6706
Polymers105,3013
Non-polymers1,3693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7920 Å2
ΔGint-46 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.194, 88.194, 165.774
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-918-

HOH

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Components

#1: Protein Phosphopantothenoylcysteine decarboxylase / HAL3


Mass: 35100.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus) / Gene: CNAG_07348 / Production host: Escherichia coli (E. coli) / References: UniProt: J9VGI2
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 291 K / Method: evaporation / Details: 0.8M Succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.18→56.17 Å / Num. obs: 12855 / % possible obs: 96.5 % / Redundancy: 9.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Net I/σ(I): 17.2
Reflection shellResolution: 2.18→2.29 Å / Redundancy: 6.9 % / Num. unique obs: 1694 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+20 / Resolution: 2.18→56.168 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.82
RfactorNum. reflection% reflection
Rfree0.2391 625 5 %
Rwork0.2144 --
obs0.2158 12512 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.18→56.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 31 20 1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041529
X-RAY DIFFRACTIONf_angle_d0.8832089
X-RAY DIFFRACTIONf_dihedral_angle_d15.625540
X-RAY DIFFRACTIONf_chiral_restr0.033243
X-RAY DIFFRACTIONf_plane_restr0.003262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1763-2.39530.32541400.28262575X-RAY DIFFRACTION83
2.3953-2.74190.34561620.26733014X-RAY DIFFRACTION97
2.7419-3.45450.33961640.26713124X-RAY DIFFRACTION99
3.4545-56.18650.19041590.18313174X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -40.9012 Å / Origin y: 6.0033 Å / Origin z: 14.3356 Å
111213212223313233
T0.64 Å20.0116 Å20.0553 Å2-0.5682 Å2-0.1067 Å2--0.6271 Å2
L2.3547 °2-0.045 °20.7223 °2-3.6386 °2-0.7146 °2--1.8604 °2
S-0.0006 Å °0.2031 Å °-0.4635 Å °-0.2928 Å °-0.0134 Å °-0.0286 Å °0.2214 Å °0.0189 Å °0.0081 Å °
Refinement TLS groupSelection details: all

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